BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 037508
(449 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
pdb|4DZS|B Chain B, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
Length = 357
Score = 178 bits (452), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 103/288 (35%), Positives = 167/288 (57%), Gaps = 12/288 (4%)
Query: 153 GNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCS 212
G+I +L KDQ+GCR LQ+ + L + + IF E D ELM D FGNY++QKL+E +
Sbjct: 35 GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 94
Query: 213 EEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTK 272
EQR +L +++ F V I LN HG RA+ KL+E + ++ +V+ +LRP V L+K
Sbjct: 95 TEQRI-VLTKISSPHF--VEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 151
Query: 273 DTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERXX 332
D NG++VIQ C++ E+ +++ + ++D+C IAT + GCCVLQ C+++ Q +
Sbjct: 152 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 211
Query: 333 XXXXXXXXXXXXDCYGNYVVQHLLALRVPQ----ITASLLRQLEGHYVSFSCNKYGSNVV 388
D +GNYVVQ+++ + T ++ L+ + S +K+GSNV+
Sbjct: 212 DKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVI 271
Query: 389 ERCLLESGEEQSTRIIIELLRS---PNVSMLLMHPFGNYVIQSALLVS 433
E+ L + S +I+E+L + + LL +GNYV+Q+AL +S
Sbjct: 272 EKILKTAI--VSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 317
>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
pdb|3BX2|B Chain B, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
Length = 335
Score = 177 bits (450), Expect = 9e-45, Method: Compositional matrix adjust.
Identities = 103/288 (35%), Positives = 166/288 (57%), Gaps = 12/288 (4%)
Query: 153 GNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCS 212
G+I +L KDQ+GCR LQ+ + L + + IF E D ELM D FGNY++QKL+E +
Sbjct: 13 GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 72
Query: 213 EEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTK 272
EQR +L +++ F V I LN HG RA+ KL+E + ++ +V+ +LRP V L+K
Sbjct: 73 TEQRI-VLTKISSPHF--VEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 273 DTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERXX 332
D NG++VIQ C++ E+ +++ + ++D+C IAT + GCCVLQ C+++ Q +
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 189
Query: 333 XXXXXXXXXXXXDCYGNYVVQHLLALRVPQ----ITASLLRQLEGHYVSFSCNKYGSNVV 388
D +GNYVVQ+++ + T ++ L+ + S +K+GSNV+
Sbjct: 190 DKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVI 249
Query: 389 ERCLLESGEEQSTRIIIELLRS---PNVSMLLMHPFGNYVIQSALLVS 433
E+ L S +I+E+L + + LL +GNYV+Q+AL +S
Sbjct: 250 EKIL--KTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 177 bits (450), Expect = 9e-45, Method: Compositional matrix adjust.
Identities = 103/288 (35%), Positives = 166/288 (57%), Gaps = 12/288 (4%)
Query: 153 GNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCS 212
G+I +L KDQ+GCR LQ+ + L + + IF E D ELM D FGNY++QKL+E +
Sbjct: 13 GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 72
Query: 213 EEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTK 272
EQR +L +++ F V I LN HG RA+ KL+E + ++ +V+ +LRP V L+K
Sbjct: 73 TEQRI-VLTKISSPHF--VEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 273 DTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERXX 332
D NG++VIQ C++ E+ +++ + ++D+C IAT + GCCVLQ C+++ Q +
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 189
Query: 333 XXXXXXXXXXXXDCYGNYVVQHLLALRVPQ----ITASLLRQLEGHYVSFSCNKYGSNVV 388
D +GNYVVQ+++ + T ++ L+ + S +K+GSNV+
Sbjct: 190 DKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVI 249
Query: 389 ERCLLESGEEQSTRIIIELLRS---PNVSMLLMHPFGNYVIQSALLVS 433
E+ L S +I+E+L + + LL +GNYV+Q+AL +S
Sbjct: 250 EKIL--KTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
pdb|3BX3|B Chain B, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
Length = 335
Score = 172 bits (436), Expect = 3e-43, Method: Compositional matrix adjust.
Identities = 102/288 (35%), Positives = 165/288 (57%), Gaps = 12/288 (4%)
Query: 153 GNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCS 212
G+I +L KDQ+GCR LQ+ + L + + IF E D ELM D FGNY++QKL+E +
Sbjct: 13 GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 72
Query: 213 EEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTK 272
EQR +L +++ F V I LN HG RA+ KL+E + ++ +V+ +LRP V L+K
Sbjct: 73 TEQRI-VLTKISSPHF--VEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 273 DTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERXX 332
D NG++VIQ C++ E+ +++ + ++D+C IAT + GC VLQ C+++ Q +
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLC 189
Query: 333 XXXXXXXXXXXXDCYGNYVVQHLLALRVPQ----ITASLLRQLEGHYVSFSCNKYGSNVV 388
D +GNYVVQ+++ + T ++ L+ + S +K+GSNV+
Sbjct: 190 DKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVI 249
Query: 389 ERCLLESGEEQSTRIIIELLRS---PNVSMLLMHPFGNYVIQSALLVS 433
E+ L S +I+E+L + + LL +GNYV+Q+AL +S
Sbjct: 250 EKIL--KTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
>pdb|3Q0Q|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With P38alpha Nrea
pdb|3Q0R|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With P38alpha Nreb
pdb|3Q0S|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With Erk2 Nre
Length = 351
Score = 140 bits (353), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 87/306 (28%), Positives = 159/306 (51%), Gaps = 13/306 (4%)
Query: 135 RNQWLQD----SFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDR 190
R++ L+D F LRDL G+IV ++DQ+G R +Q+ + E +M+F E++
Sbjct: 2 RSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQA 61
Query: 191 VCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENL 250
+LM D FGNYV+QK E S +Q+ L + T ++ + L +G R + K LE++
Sbjct: 62 AYQLMTDVFGNYVIQKFFEFGSLDQK---LALATRIRGHVLPLALQMYGCRVIQKALESI 118
Query: 251 TNPQQ-ISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATD 309
++ QQ IS ++ L + KD NG++V+Q C++ + +++++ + ++T
Sbjct: 119 SSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTH 178
Query: 310 KSGCCVLQHCVEYSKGAQRERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQITASLLR 369
GC V+Q +E+ Q D YGNYV+QH+L P+ + ++
Sbjct: 179 PYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVS 238
Query: 370 QLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELL---RSPNVSMLLMHP--FGNY 424
++ G ++ S +K+ SNVVE+C+ + + +I E+ P+ ++ M + NY
Sbjct: 239 EIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANY 298
Query: 425 VIQSAL 430
V+Q +
Sbjct: 299 VVQKMI 304
Score = 88.2 bits (217), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 69/273 (25%), Positives = 127/273 (46%), Gaps = 24/273 (8%)
Query: 136 NQWLQDSFDCSSLRD-------LRGNIVALAKDQYGCRHLQRTMSSLPKEE--IEMIFVE 186
N +Q F+ SL +RG+++ LA YGCR +Q+ + S+ ++ I + E
Sbjct: 72 NYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKE 131
Query: 187 VIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTH--GIRAVL 244
+ V + + D GN+VVQK +E C + Q + ++ D F+ L+TH G R +
Sbjct: 132 LDGHVLKCVKDQNGNHVVQKCIE-CVQPQSLQFII----DAFKGQVFVLSTHPYGCRVIQ 186
Query: 245 KLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCY 304
++LE+ T Q + +L L L +D G+YVIQ+ ++H ED +++E+
Sbjct: 187 RILEHCTAEQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVL 245
Query: 305 GIATDKSGCCVLQHCVEYSKGAQRERXXXXX-------XXXXXXXXXDCYGNYVVQHLLA 357
++ K V++ CV ++ A+R D Y NYVVQ ++
Sbjct: 246 ALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMID 305
Query: 358 LRVPQITASLLRQLEGHYVSFSCNKYGSNVVER 390
+ P ++ ++ H + YG +++ +
Sbjct: 306 MAEPAQRKIIMHKIRPHITTLRKYTYGKHILAK 338
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 44/191 (23%), Positives = 81/191 (42%), Gaps = 49/191 (25%)
Query: 137 QWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMI 196
Q++ D+F +G + L+ YGCR +QR + E+ I E+ +L+
Sbjct: 162 QFIIDAF--------KGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQ 213
Query: 197 DPFGNYVVQKLVELCSEEQRTRIL-------LMLTNDDF--QLVRICLNTHGIRA----- 242
D +GNYV+Q ++E E +++I+ L L+ F +V C+ TH RA
Sbjct: 214 DQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCV-THASRAERALL 272
Query: 243 --------------------------VLKLLENLTNPQQISLVLAALRPGAVTLTKDTNG 276
V++ + ++ P Q +++ +RP TL K T G
Sbjct: 273 IDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYG 332
Query: 277 HYVIQYCVKHF 287
+++ K++
Sbjct: 333 KHILAKLEKYY 343
>pdb|3K49|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K49|C Chain C, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K49|E Chain E, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K4E|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
pdb|3K4E|C Chain C, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
pdb|3K4E|E Chain E, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
Length = 369
Score = 139 bits (351), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 95/306 (31%), Positives = 157/306 (51%), Gaps = 25/306 (8%)
Query: 148 LRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKL 207
L+D+ G+ + KDQ+G R +QR +++ P E E+IF E+ D EL D FGNYV+QK
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 208 VELCSEEQRTRILLMLTNDDFQ--LVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRP 265
E S+ Q+ ++ D F+ + ++ L + R + K LE + + Q+I LVL L
Sbjct: 86 FEFGSKIQKNTLV-----DQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVL-ELSD 139
Query: 266 GAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKG 325
+ + KD NG++VIQ ++ E ++L+ + + Y ++T GC V+Q +E+
Sbjct: 140 SVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSS 199
Query: 326 AQRERXXXXXXXXXXXXXXDCYGNYVVQHLLAL------RVPQITASLLRQLEGHYVSFS 379
+E D YGNYV+Q++L + I ++ + + V +S
Sbjct: 200 EDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYS 259
Query: 380 CNKYGSNVVERCLLESGEEQSTRIIIELL-RSPNVS--------MLLM--HPFGNYVIQS 428
+K+ SNVVE+ +L + Q II ++L R N + M+LM F NYVIQ
Sbjct: 260 KHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQK 319
Query: 429 ALLVSK 434
+ VS+
Sbjct: 320 LVNVSE 325
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 48/105 (45%), Gaps = 21/105 (20%)
Query: 140 QDSFDCSSLRDLR--------GNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVI--- 188
QD F + D++ N+V +K ++ +++++ K + ++I +++
Sbjct: 232 QDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKILPRD 291
Query: 189 ---------DRVCELMI-DPFGNYVVQKLVELCSEEQRTRILLML 223
D LMI D F NYV+QKLV + E + I++ +
Sbjct: 292 KNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVIAI 336
>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain)
pdb|3H3D|Y Chain Y, Drosophila Pumilio Rna Binding Domain (Puf Domain)
Length = 323
Score = 139 bits (350), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 83/289 (28%), Positives = 146/289 (50%), Gaps = 6/289 (2%)
Query: 148 LRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKL 207
LRDL +IV ++DQ+G R +Q+ + E +M+F E++ LM D FGNYV+QK
Sbjct: 21 LRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKF 80
Query: 208 VELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGA 267
E + EQ+ + + + QL L +G R + K LE+++ P+Q ++ L
Sbjct: 81 FEFGTPEQKNTLGMQVKGHVLQL---ALQMYGCRVIQKALESIS-PEQQQEIVHELDGHV 136
Query: 268 VTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQ 327
+ KD NG++V+Q C++ ++++N Y ++T GC V+Q +E+ Q
Sbjct: 137 LKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQ 196
Query: 328 RERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNV 387
D YGNYV+QH+L + + L+ + G + S +K+ SNV
Sbjct: 197 TTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 256
Query: 388 VERCLLESGEEQSTRIIIEL--LRSPNVSMLLMHPFGNYVIQSALLVSK 434
VE+C+ + + T +I E+ + +++ + NYV+Q + VS+
Sbjct: 257 VEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSE 305
Score = 82.0 bits (201), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 62/227 (27%), Positives = 110/227 (48%), Gaps = 12/227 (5%)
Query: 151 LRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVEL 210
++G+++ LA YGCR +Q+ + S+ E+ + I E+ V + + D GN+VVQK +E
Sbjct: 96 VKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIE- 154
Query: 211 CSEEQRTRILLMLTNDDFQLVRICLNTH--GIRAVLKLLENLTNPQQISLVLAALRPGAV 268
C + + L + F+ L+TH G R + ++LE+ T +Q + +L L
Sbjct: 155 CVDP----VALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCT-AEQTTPILDELHEHTE 209
Query: 269 TLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQR 328
L +D G+YVIQ+ ++H ED L+N V ++ K V++ CV ++ +R
Sbjct: 210 QLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGER 269
Query: 329 ----ERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQITASLLRQL 371
+ D Y NYVVQ ++ + P L+ ++
Sbjct: 270 TGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKI 316
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/123 (19%), Positives = 55/123 (44%)
Query: 148 LRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKL 207
L +L + L +DQYG +Q + +E+ ++ V +V L F + VV+K
Sbjct: 201 LDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKC 260
Query: 208 VELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGA 267
V + +RT ++ + + + + + V++ + +++ P Q+ ++ +R
Sbjct: 261 VTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRKNM 320
Query: 268 VTL 270
L
Sbjct: 321 AAL 323
>pdb|3GVO|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
pdb|3GVT|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
pdb|3GVT|B Chain B, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
Length = 351
Score = 137 bits (345), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 85/305 (27%), Positives = 157/305 (51%), Gaps = 13/305 (4%)
Query: 135 RNQWLQD----SFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDR 190
R++ L+D F LRDL G+IV ++DQ+G R +Q+ + E +++F E++
Sbjct: 4 RSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQA 63
Query: 191 VCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENL 250
+LM D FGNYV+QK E S +Q+ L + T ++ + L +G R + K LE++
Sbjct: 64 AYQLMTDVFGNYVIQKFFEFGSLDQK---LALATRIRGHVLPLALQMYGCRVIQKALESI 120
Query: 251 TNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDK 310
++ QQ +V L + KD NG++V+Q C++ + +++++ + ++T
Sbjct: 121 SSDQQSEMV-KELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHP 179
Query: 311 SGCCVLQHCVEYSKGAQRERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQITASLLRQ 370
GC V+Q +E+ Q D YGNYV+QH+L P+ + ++ +
Sbjct: 180 YGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSE 239
Query: 371 LEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELL---RSPNVSMLLMHP--FGNYV 425
+ G ++ S +K+ SNVVE+C+ + + +I E+ P+ ++ M + NYV
Sbjct: 240 IRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYV 299
Query: 426 IQSAL 430
+Q +
Sbjct: 300 VQKMI 304
Score = 90.1 bits (222), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 68/271 (25%), Positives = 126/271 (46%), Gaps = 22/271 (8%)
Query: 136 NQWLQDSFDCSSLRD-------LRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVI 188
N +Q F+ SL +RG+++ LA YGCR +Q+ + S+ ++ + E+
Sbjct: 74 NYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELD 133
Query: 189 DRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTH--GIRAVLKL 246
V + + D GN+VVQK +E C + Q + ++ D F+ L+TH G R + ++
Sbjct: 134 GHVLKCVKDQNGNHVVQKCIE-CVQPQSLQFII----DAFKGQVFVLSTHPYGCRVIQRI 188
Query: 247 LENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGI 306
LE+ T Q + +L L L +D G+YVIQ+ ++H ED +++E+ +
Sbjct: 189 LEHCTAEQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLAL 247
Query: 307 ATDKSGCCVLQHCVEYSKGAQRERXXXXX-------XXXXXXXXXDCYGNYVVQHLLALR 359
+ K V++ CV ++ A+R D Y NYVVQ ++ +
Sbjct: 248 SQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMA 307
Query: 360 VPQITASLLRQLEGHYVSFSCNKYGSNVVER 390
P ++ ++ H + YG +++ +
Sbjct: 308 EPAQRKIIMHKIRPHITTLRKYTYGKHILAK 338
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 51/234 (21%), Positives = 98/234 (41%), Gaps = 54/234 (23%)
Query: 95 NQDSSILNLLHNHNFDGLR-SNGNELSSVPRNQWMSSLSLKRNQWLQDSFDCSSLRDLRG 153
+Q S ++ L H ++ NGN + + + + + Q++ D+F +G
Sbjct: 123 DQQSEMVKELDGHVLKCVKDQNGNHVV----QKCIECVQPQSLQFIIDAF--------KG 170
Query: 154 NIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSE 213
+ L+ YGCR +QR + E+ I E+ +L+ D +GNYV+Q ++E
Sbjct: 171 QVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRP 230
Query: 214 EQRTRIL-------LMLTNDDF--QLVRICLNTHGIRA---------------------- 242
E +++I+ L L+ F +V C+ TH RA
Sbjct: 231 EDKSKIVSEIRGKVLALSQHKFASNVVEKCV-THASRAERALLIDEVCCQNDGPHSALYT 289
Query: 243 ---------VLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHF 287
V++ + ++ P Q +++ +RP TL K T G +++ K++
Sbjct: 290 MMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYY 343
>pdb|3BSB|A Chain A, Crystal Structure Of Human Pumilio1 In Complex With
Cyclinb Reverse Rna
pdb|3BSB|B Chain B, Crystal Structure Of Human Pumilio1 In Complex With
Cyclinb Reverse Rna
pdb|3BSX|A Chain A, Crystal Structure Of Human Pumilio 1 In Complex With Puf5
Rna
pdb|3BSX|B Chain B, Crystal Structure Of Human Pumilio 1 In Complex With Puf5
Rna
Length = 343
Score = 129 bits (324), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 79/293 (26%), Positives = 150/293 (51%), Gaps = 9/293 (3%)
Query: 147 SLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQK 206
LR++ G+I+ ++DQ+G R +Q + E +++F E++ +LM+D FGNYV+QK
Sbjct: 18 QLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQK 77
Query: 207 LVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPG 266
E S EQ+ L + ++ + L +G R + K LE + + QQ +V L
Sbjct: 78 FFEFGSLEQK---LALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV-RELDGH 133
Query: 267 AVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGA 326
+ KD NG++V+Q C++ + +++++ + ++T GC V+Q +E+
Sbjct: 134 VLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPD 193
Query: 327 QRERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSN 386
Q D YGNYV+QH+L P+ + ++ ++ G+ + S +K+ SN
Sbjct: 194 QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASN 253
Query: 387 VVERCLLESGEEQSTRIIIELLR---SPNVSMLLMHP--FGNYVIQSALLVSK 434
VVE+C+ + + +I E+ P+ ++ M + NYV+Q + V++
Sbjct: 254 VVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAE 306
Score = 88.2 bits (217), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 68/271 (25%), Positives = 125/271 (46%), Gaps = 22/271 (8%)
Query: 136 NQWLQDSFDCSSLRD-------LRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVI 188
N +Q F+ SL +RG++++LA YGCR +Q+ + +P ++ + E+
Sbjct: 72 NYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELD 131
Query: 189 DRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTH--GIRAVLKL 246
V + + D GN+VVQK +E C + Q + ++ D F+ L+TH G R + ++
Sbjct: 132 GHVLKCVKDQNGNHVVQKCIE-CVQPQSLQFII----DAFKGQVFALSTHPYGCRVIQRI 186
Query: 247 LENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGI 306
LE+ P Q +L L L +D G+YVIQ+ ++H ED ++ E+ N +
Sbjct: 187 LEHCL-PDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVL 245
Query: 307 ATDKSGCCVLQHCVEYSKGAQRERXXXXX-------XXXXXXXXXDCYGNYVVQHLLALR 359
+ K V++ CV ++ +R D Y NYVVQ ++ +
Sbjct: 246 SQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVA 305
Query: 360 VPQITASLLRQLEGHYVSFSCNKYGSNVVER 390
P ++ ++ H + YG +++ +
Sbjct: 306 EPGQRKIVMHKIRPHIATLRKYTYGKHILAK 336
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 46/186 (24%), Positives = 84/186 (45%), Gaps = 2/186 (1%)
Query: 245 KLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCY 304
+LLE+ N + +L L + + ++D +G IQ ++ + + + + NE+ Y
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 305 GIATDKSGCCVLQHCVEYSKGAQRERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQIT 364
+ D G V+Q E+ Q+ YG V+Q L
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 123
Query: 365 ASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNY 424
++R+L+GH + ++ G++VV++C +E + QS + II+ + V L HP+G
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKC-IECVQPQSLQFIIDAFKG-QVFALSTHPYGCR 181
Query: 425 VIQSAL 430
VIQ L
Sbjct: 182 VIQRIL 187
>pdb|1IB2|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8Z|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8W|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8W|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8X|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8X|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8Y|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|1M8Y|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|3Q0L|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0L|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0M|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0M|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0N|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0N|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0P|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
pdb|3Q0P|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
Length = 349
Score = 129 bits (324), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 79/293 (26%), Positives = 150/293 (51%), Gaps = 9/293 (3%)
Query: 147 SLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQK 206
LR++ G+I+ ++DQ+G R +Q + E +++F E++ +LM+D FGNYV+QK
Sbjct: 18 QLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQK 77
Query: 207 LVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPG 266
E S EQ+ L + ++ + L +G R + K LE + + QQ +V L
Sbjct: 78 FFEFGSLEQK---LALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV-RELDGH 133
Query: 267 AVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGA 326
+ KD NG++V+Q C++ + +++++ + ++T GC V+Q +E+
Sbjct: 134 VLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPD 193
Query: 327 QRERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSN 386
Q D YGNYV+QH+L P+ + ++ ++ G+ + S +K+ SN
Sbjct: 194 QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASN 253
Query: 387 VVERCLLESGEEQSTRIIIELLR---SPNVSMLLMHP--FGNYVIQSALLVSK 434
VVE+C+ + + +I E+ P+ ++ M + NYV+Q + V++
Sbjct: 254 VVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAE 306
Score = 88.2 bits (217), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 68/271 (25%), Positives = 125/271 (46%), Gaps = 22/271 (8%)
Query: 136 NQWLQDSFDCSSLRD-------LRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVI 188
N +Q F+ SL +RG++++LA YGCR +Q+ + +P ++ + E+
Sbjct: 72 NYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELD 131
Query: 189 DRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTH--GIRAVLKL 246
V + + D GN+VVQK +E C + Q + ++ D F+ L+TH G R + ++
Sbjct: 132 GHVLKCVKDQNGNHVVQKCIE-CVQPQSLQFII----DAFKGQVFALSTHPYGCRVIQRI 186
Query: 247 LENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGI 306
LE+ P Q +L L L +D G+YVIQ+ ++H ED ++ E+ N +
Sbjct: 187 LEHCL-PDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVL 245
Query: 307 ATDKSGCCVLQHCVEYSKGAQRERXXXXX-------XXXXXXXXXDCYGNYVVQHLLALR 359
+ K V++ CV ++ +R D Y NYVVQ ++ +
Sbjct: 246 SQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVA 305
Query: 360 VPQITASLLRQLEGHYVSFSCNKYGSNVVER 390
P ++ ++ H + YG +++ +
Sbjct: 306 EPGQRKIVMHKIRPHIATLRKYTYGKHILAK 336
Score = 58.2 bits (139), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 46/186 (24%), Positives = 84/186 (45%), Gaps = 2/186 (1%)
Query: 245 KLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCY 304
+LLE+ N + +L L + + ++D +G IQ ++ + + + + NE+ Y
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 305 GIATDKSGCCVLQHCVEYSKGAQRERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQIT 364
+ D G V+Q E+ Q+ YG V+Q L
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 123
Query: 365 ASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNY 424
++R+L+GH + ++ G++VV++C +E + QS + II+ + V L HP+G
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKC-IECVQPQSLQFIIDAFKG-QVFALSTHPYGCR 181
Query: 425 VIQSAL 430
VIQ L
Sbjct: 182 VIQRIL 187
>pdb|2YJY|A Chain A, A Specific And Modular Binding Code For Cytosine
Recognition In Puf Domains
pdb|2YJY|B Chain B, A Specific And Modular Binding Code For Cytosine
Recognition In Puf Domains
Length = 350
Score = 125 bits (314), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 77/293 (26%), Positives = 150/293 (51%), Gaps = 9/293 (3%)
Query: 147 SLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQK 206
LR++ G+I+ ++DQ+G R +Q + E +++F E++ +LM+D FGNYV+QK
Sbjct: 19 QLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQK 78
Query: 207 LVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPG 266
E S EQ+ L + ++ + L +G R + K LE + + QQ +V L
Sbjct: 79 FFEFGSLEQK---LALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV-RELDGH 134
Query: 267 AVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGA 326
+ KD NG++V+Q C++ + +++++ + ++T GC V+Q +E+
Sbjct: 135 VLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPD 194
Query: 327 QRERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSN 386
Q D YG+YV++H+L P+ + ++ ++ G+ + S +K+ SN
Sbjct: 195 QTLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASN 254
Query: 387 VVERCLLESGEEQSTRIIIELLR---SPNVSMLLMHP--FGNYVIQSALLVSK 434
VVE+C+ + + +I E+ P+ ++ M + NYV+Q + V++
Sbjct: 255 VVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAE 307
Score = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 67/271 (24%), Positives = 124/271 (45%), Gaps = 22/271 (8%)
Query: 136 NQWLQDSFDCSSLRD-------LRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVI 188
N +Q F+ SL +RG++++LA YGCR +Q+ + +P ++ + E+
Sbjct: 73 NYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELD 132
Query: 189 DRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTH--GIRAVLKL 246
V + + D GN+VVQK +E C + Q + ++ D F+ L+TH G R + ++
Sbjct: 133 GHVLKCVKDQNGNHVVQKCIE-CVQPQSLQFII----DAFKGQVFALSTHPYGCRVIQRI 187
Query: 247 LENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGI 306
LE+ P Q +L L L +D G YVI++ ++H ED ++ E+ N +
Sbjct: 188 LEHCL-PDQTLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVL 246
Query: 307 ATDKSGCCVLQHCVEYSKGAQRERXXXXX-------XXXXXXXXXDCYGNYVVQHLLALR 359
+ K V++ CV ++ +R D Y NYVVQ ++ +
Sbjct: 247 SQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVA 306
Query: 360 VPQITASLLRQLEGHYVSFSCNKYGSNVVER 390
P ++ ++ H + YG +++ +
Sbjct: 307 EPGQRKIVMHKIRPHIATLRKYTYGKHILAK 337
Score = 58.2 bits (139), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 46/186 (24%), Positives = 84/186 (45%), Gaps = 2/186 (1%)
Query: 245 KLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCY 304
+LLE+ N + +L L + + ++D +G IQ ++ + + + + NE+ Y
Sbjct: 5 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 64
Query: 305 GIATDKSGCCVLQHCVEYSKGAQRERXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQIT 364
+ D G V+Q E+ Q+ YG V+Q L
Sbjct: 65 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 124
Query: 365 ASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNY 424
++R+L+GH + ++ G++VV++C +E + QS + II+ + V L HP+G
Sbjct: 125 NEMVRELDGHVLKCVKDQNGNHVVQKC-IECVQPQSLQFIIDAFKG-QVFALSTHPYGCR 182
Query: 425 VIQSAL 430
VIQ L
Sbjct: 183 VIQRIL 188
>pdb|3QG9|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea A7u Mutant Complex
pdb|3V6Y|A Chain A, Crystal Structure Of Fbf-2 In Complex With A Mutant Gld-1
Fbea13 Rna
pdb|3V74|A Chain A, Crystal Structure Of Fbf-2 In Complex With Gld-1 Fbea13
Rna
Length = 413
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 89/360 (24%), Positives = 157/360 (43%), Gaps = 67/360 (18%)
Query: 125 NQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTM-SSLPKEEIEMI 183
N + + SL N ++ S + D G+++ A D+ GC+ L++ + SL + +
Sbjct: 3 NNVLPTWSLDSNGEMRSRLSLSEVLD-SGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQL 61
Query: 184 FVEVI---DRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDD------------- 227
F +VI D +L + FGNY+VQ ++ + + TNDD
Sbjct: 62 FEQVIGRKDDFLKLSTNIFGNYLVQSVIGIS----------LATNDDGYTKRQEKLKNFI 111
Query: 228 -FQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPG-AVTLTKDTNGHYVIQYCVK 285
Q+ +CL+ R + L+N+ LV A R + + D N ++VIQ V
Sbjct: 112 SSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVA 171
Query: 286 HFSHEDTKYLLNEVA--DNCYGIATDKSGCCVLQHCVE----------YSKGAQ--RERX 331
++ +++++ VA ++ I +DK GC V+Q +E + AQ RER
Sbjct: 172 VIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERA 231
Query: 332 XXXXXXXXXXXXXDC----YGNYVVQHLLA------LRVPQITASLLRQLEGHYVSFSCN 381
+ Y NY++QH+++ R I L+R L +S S
Sbjct: 232 LQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNL----LSLSQE 287
Query: 382 KYGSNVVERCLLESGEEQSTRIIIELLRS----PN-----VSMLLMHPFGNYVIQSALLV 432
K+ S+VVE+ L + E ++ E+ P+ + +++ H FGNYV+Q L +
Sbjct: 288 KFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTI 347
>pdb|3K5Q|A Chain A, Crystal Structure Of Fbf-2FBE COMPLEX
pdb|3K5Y|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea Complex
pdb|3K5Z|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea G4a Mutant Complex
pdb|3K61|A Chain A, Crystal Structure Of Fbf-2FOG-1 Fbea Complex
pdb|3K62|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbeb Complex
pdb|3K64|A Chain A, Crystal Structure Of Fbf-2FEM-3 Pme Complex
Length = 412
Score = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 89/360 (24%), Positives = 157/360 (43%), Gaps = 67/360 (18%)
Query: 125 NQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTM-SSLPKEEIEMI 183
N + + SL N ++ S + D G+++ A D+ GC+ L++ + SL + +
Sbjct: 2 NNVLPTWSLDSNGEMRSRLSLSEVLD-SGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQL 60
Query: 184 FVEVI---DRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDD------------- 227
F +VI D +L + FGNY+VQ ++ + + TNDD
Sbjct: 61 FEQVIGRKDDFLKLSTNIFGNYLVQSVIGIS----------LATNDDGYTKRQEKLKNFI 110
Query: 228 -FQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPG-AVTLTKDTNGHYVIQYCVK 285
Q+ +CL+ R + L+N+ LV A R + + D N ++VIQ V
Sbjct: 111 SSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVA 170
Query: 286 HFSHEDTKYLLNEVA--DNCYGIATDKSGCCVLQHCVE----------YSKGAQ--RERX 331
++ +++++ VA ++ I +DK GC V+Q +E + AQ RER
Sbjct: 171 VIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERA 230
Query: 332 XXXXXXXXXXXXXDC----YGNYVVQHLLA------LRVPQITASLLRQLEGHYVSFSCN 381
+ Y NY++QH+++ R I L+R L +S S
Sbjct: 231 LQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNL----LSLSQE 286
Query: 382 KYGSNVVERCLLESGEEQSTRIIIELLRS----PN-----VSMLLMHPFGNYVIQSALLV 432
K+ S+VVE+ L + E ++ E+ P+ + +++ H FGNYV+Q L +
Sbjct: 287 KFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTI 346
>pdb|3QGB|A Chain A, Crystal Structure Of Fbf-2 R288y Mutant In Complex With
Gld-1 Fbea
pdb|3QGC|A Chain A, Crystal Structure Of Fbf-2 R288y Mutant In Complex With
Gld-1 Fbea A7u Mutant
Length = 413
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 88/360 (24%), Positives = 156/360 (43%), Gaps = 67/360 (18%)
Query: 125 NQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTM-SSLPKEEIEMI 183
N + + SL N ++ S + D G+++ A D+ GC+ L++ + SL + +
Sbjct: 3 NNVLPTWSLDSNGEMRSRLSLSEVLD-SGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQL 61
Query: 184 FVEVI---DRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDD------------- 227
F +VI D +L + FGNY+VQ ++ + + TNDD
Sbjct: 62 FEQVIGRKDDFLKLSTNIFGNYLVQSVIGIS----------LATNDDGYTKRQEKLKNFI 111
Query: 228 -FQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPG-AVTLTKDTNGHYVIQYCVK 285
Q+ +CL+ + L+N+ LV A R + + D N ++VIQ V
Sbjct: 112 SSQMTDMCLDKFACYVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVA 171
Query: 286 HFSHEDTKYLLNEVA--DNCYGIATDKSGCCVLQHCVE----------YSKGAQ--RERX 331
++ +++++ VA ++ I +DK GC V+Q +E + AQ RER
Sbjct: 172 VIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERA 231
Query: 332 XXXXXXXXXXXXXDC----YGNYVVQHLLA------LRVPQITASLLRQLEGHYVSFSCN 381
+ Y NY++QH+++ R I L+R L +S S
Sbjct: 232 LQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNL----LSLSQE 287
Query: 382 KYGSNVVERCLLESGEEQSTRIIIELLRS----PN-----VSMLLMHPFGNYVIQSALLV 432
K+ S+VVE+ L + E ++ E+ P+ + +++ H FGNYV+Q L +
Sbjct: 288 KFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTI 347
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 55.1 bits (131), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 78/327 (23%), Positives = 132/327 (40%), Gaps = 43/327 (13%)
Query: 147 SLRD--LRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPF----G 200
SL D L G ++ A D G + L+ +++I E L + G
Sbjct: 12 SLEDVLLNGQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNG 71
Query: 201 NYVVQKLVELCS-EEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLV 259
N++VQKLVEL + EQR + M+ D L+ +C + R V L+ + L+
Sbjct: 72 NFIVQKLVELATPAEQRELLRQMI---DGGLLAMCKDKFACRVVQLALQKFDHSNVFQLI 128
Query: 260 LAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVA--DNCYGIATDKSGCCVLQ 317
+ D +VIQ VK + + ++ ++ D+ + DK GC ++Q
Sbjct: 129 QELSTFDLAAMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQ 188
Query: 318 HCV----EYSKGAQRERXXXXXXXXXXXXXXDCY-------GNYVVQHLLA-------LR 359
+ E K + +CY NYV+Q+++ R
Sbjct: 189 QVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYR 248
Query: 360 VPQITASLLRQLEGHYVSFSCNKYGSNVVERCLL--------ESGEEQSTRIIIELLRSP 411
I LLR L +S S +KY S+V+E L E EE + + ++ +
Sbjct: 249 DTIIDKCLLRNL----LSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNR 304
Query: 412 N-VSMLLMHPFGNYVIQSALLVSKVRL 437
+ + +LL H +GNYV+Q + + L
Sbjct: 305 DALDILLFHQYGNYVVQQMISICTAAL 331
>pdb|1GUL|A Chain A, Human Glutathione Transferase A4-4 Complex With Iodobenzyl
Glutathione
pdb|1GUL|B Chain B, Human Glutathione Transferase A4-4 Complex With Iodobenzyl
Glutathione
pdb|1GUL|C Chain C, Human Glutathione Transferase A4-4 Complex With Iodobenzyl
Glutathione
pdb|1GUL|D Chain D, Human Glutathione Transferase A4-4 Complex With Iodobenzyl
Glutathione
pdb|1GUL|E Chain E, Human Glutathione Transferase A4-4 Complex With Iodobenzyl
Glutathione
pdb|1GUL|F Chain F, Human Glutathione Transferase A4-4 Complex With Iodobenzyl
Glutathione
pdb|1GUL|G Chain G, Human Glutathione Transferase A4-4 Complex With Iodobenzyl
Glutathione
pdb|1GUL|H Chain H, Human Glutathione Transferase A4-4 Complex With Iodobenzyl
Glutathione
pdb|1GUM|A Chain A, Human Glutathione Transferase A4-4 Without Ligands
pdb|1GUM|B Chain B, Human Glutathione Transferase A4-4 Without Ligands
pdb|1GUM|C Chain C, Human Glutathione Transferase A4-4 Without Ligands
pdb|1GUM|D Chain D, Human Glutathione Transferase A4-4 Without Ligands
pdb|1GUM|E Chain E, Human Glutathione Transferase A4-4 Without Ligands
pdb|1GUM|F Chain F, Human Glutathione Transferase A4-4 Without Ligands
pdb|1GUM|G Chain G, Human Glutathione Transferase A4-4 Without Ligands
pdb|1GUM|H Chain H, Human Glutathione Transferase A4-4 Without Ligands
pdb|3IK7|A Chain A, Human Glutathione Transferase A4-4 With Gsdhn
pdb|3IK7|B Chain B, Human Glutathione Transferase A4-4 With Gsdhn
pdb|3IK7|C Chain C, Human Glutathione Transferase A4-4 With Gsdhn
pdb|3IK7|D Chain D, Human Glutathione Transferase A4-4 With Gsdhn
Length = 222
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 13/72 (18%)
Query: 354 HLLALRVPQITASLLRQLEG----HYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLR 409
HLL +VP + ++ ++ HY++ N +G N+ ER L++ E + ++
Sbjct: 49 HLLFQQVPMVEIDGMKLVQTRSILHYIADKHNLFGKNLKERTLIDMYVEGTLDLL----- 103
Query: 410 SPNVSMLLMHPF 421
+L+MHPF
Sbjct: 104 ----ELLIMHPF 111
>pdb|3B0C|T Chain T, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-W
Complex, Crystal Form I
pdb|3B0D|T Chain T, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-W
Complex, Crystal Form Ii
pdb|3B0D|B Chain B, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-W
Complex, Crystal Form Ii
Length = 111
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 359 RVPQITASLLRQLEGHYVSFSCNKYGSNVVERC 391
R P+I +SL++Q+ HYV + +VE+C
Sbjct: 4 REPEIASSLIKQIFSHYVKTPVTRDAYKIVEKC 36
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.136 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,874,890
Number of Sequences: 62578
Number of extensions: 499862
Number of successful extensions: 1305
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1078
Number of HSP's gapped (non-prelim): 56
length of query: 449
length of database: 14,973,337
effective HSP length: 102
effective length of query: 347
effective length of database: 8,590,381
effective search space: 2980862207
effective search space used: 2980862207
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)